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YAPSA

Yet Another Package for Signature Analysis


Bioconductor version: Release (3.18)

This package provides functions and routines for supervised analyses of mutational signatures (i.e., the signatures have to be known, cf. L. Alexandrov et al., Nature 2013 and L. Alexandrov et al., Bioaxiv 2018). In particular, the family of functions LCD (LCD = linear combination decomposition) can use optimal signature-specific cutoffs which takes care of different detectability of the different signatures. Moreover, the package provides different sets of mutational signatures, including the COSMIC and PCAWG SNV signatures and the PCAWG Indel signatures; the latter infering that with YAPSA, the concept of supervised analysis of mutational signatures is extended to Indel signatures. YAPSA also provides confidence intervals as computed by profile likelihoods and can perform signature analysis on a stratified mutational catalogue (SMC = stratify mutational catalogue) in order to analyze enrichment and depletion patterns for the signatures in different strata.

Author: Daniel Huebschmann [aut], Lea Jopp-Saile [aut], Carolin Andresen [aut], Zuguang Gu [aut, cre], Matthias Schlesner [aut]

Maintainer: Zuguang Gu <z.gu at dkfz.de>

Citation (from within R, enter citation("YAPSA")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("YAPSA")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("YAPSA")
1. Usage of YAPSA HTML R Script
2. Signature-specific cutoffs HTML R Script
3. Confidence Intervals HTML R Script
4. Stratified Analysis of Mutational Signatures HTML R Script
5. Indel signature analysis HTML R Script
6. Usage of YAPSA for WES data HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews BiologicalQuestion, Clustering, DNASeq, GenomicVariation, Sequencing, Software, SomaticMutation, StatisticalMethod, Visualization
Version 1.28.0
In Bioconductor since BioC 3.4 (R-3.3) (7.5 years)
License GPL-3
Depends R (>= 4.0.0), GenomicRanges, ggplot2, grid
Imports limSolve, SomaticSignatures, VariantAnnotation, GenomeInfoDb, reshape2, gridExtra, corrplot, dendextend, GetoptLong, circlize, gtrellis, doParallel, parallel, PMCMRplus, ggbeeswarm, ComplexHeatmap, KEGGREST, grDevices, Biostrings, BSgenome.Hsapiens.UCSC.hg19, magrittr, pracma, dplyr, utils
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Suggests testthat, BiocStyle, knitr, rmarkdown
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package YAPSA_1.28.0.tar.gz
Windows Binary YAPSA_1.28.0.zip (64-bit only)
macOS Binary (x86_64) YAPSA_1.28.0.tgz
macOS Binary (arm64) YAPSA_1.28.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/YAPSA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/YAPSA
Bioc Package Browser https://code.bioconductor.org/browse/YAPSA/
Package Short Url https://bioconductor.org/packages/YAPSA/
Package Downloads Report Download Stats